[gmx-users] ATB server (charge assign)

[elham tazikeh]

Dear Justin
thanks for your good advise
as you're mentioned, i must include necessary file next to other force
field files in my directory
my version of gromaces is 4.6.5, and my force field is gromos 53a6

1-concerning below message, which ones is appropriate for me?
Gromacs3.x.x-4.0.x 53a6-54a7
or
Gromacs 4.5.x-5.x.x53a6

2-also, United-Atom PDB (original geometry)
<https://atb.uq.edu.au/download.py?ffVersion=53A6&file=pdb_uniatom_unoptimised&hash=HEAD&outputType=top&molid=26014>
will
be (*.pdb ) and needs to editconf to convert ( *.gro)...coordinate file
and
GROMACS G53A6FF United-Atom (ITP file)
<https://atb.uq.edu.au/download.py?ffVersion=53A6&file=rtp_uniatom&hash=HEAD&outputType=top&molid=26014>
will
be (*.itp)....topology file

Is it right?

3-coud you please tell me, when i should get those files (*.pdb and *.itp)?
before include proposed new files in my directory or after that?

Regards
elham

Warning! This molecule contains non-standard atom types not included in the
standard GROMOS 53A6 and 54A7 forcefield. To use these atom types the
internal GROMACS parameter files must be updated. These can be downloaded
using the link below. Instructions on where to place (and how to use) the
files are provided in the README file included in the archive.

Gromacs 3.x.x-4.0.x 53a6 - 54a7
<https://atb.uq.edu.au/forcefield_files/atb_gromacs/3/top_atb.tar.gz> Gromacs
4.5.x-5.x.x 53a6
<https://atb.uq.edu.au/forcefield_files/atb_gromacs/5/gromos53a6_atb.ff.tar.gz>